Antibiotic Resistance Identification By Assembly

For how to use ARIBA, please see the [ARIBA wiki page] ARIBA wiki.

ARIBA has the following dependencies, which need to be installed:

• bowtie2 Bowtie2 version >= 2.1.0
• [cd-hit] cdhit version >= 4.6
• [samtools and bcftools] samtools version >= 1.2
• MUMmer mummer version >= 3.23
• Either SPAdes spades version >= 3.5.0 or Velvet velvet version >= 1.2.07 (SPAdes is recommended)

ARIBA has the following optional dependencies. If they are installed, they will be used. Otherwise scaffolding and gap filling will be skipped.

• [SSPACE-basic scaffolder] sspace
• GapFiller gapfiller

Once the dependencies are installed, install ARIBA using pip:

pip3 install ariba

Alternatively, you can download the latest release from this github repository, or clone the repository. Then run the tests:

python3 setup.py test

If the tests all pass, install:

python3 setup.py install

Please read the [ARIBA wiki page] ARIBA wiki for usage instructions.